request help- namd error abortion stack error

From: Odysseas Axillews (blackmask1928_at_yahoo.gr)
Date: Sun Mar 21 2010 - 20:24:30 CDT

hello everyone!
i am a quite old but not very experienced user of namd and a newcomer to mailing list. I am really happy to be in this group, I would also like to contribute.
I have the following problem. I have recently obtained a new system with the following configutration
1. intel core i 5
2. asus motherboard
3.gpu ati 4350
4. 4 gb ram
5 1TB w.digital hard disk
6. scientific linux 5.4 operating system
all my simulations become aborted after 300000-700000 steps (every step 2 fs)
i get the following error in the log file before the abortion
[1] Stack Traceback:
  [0] /lib64/libc.so.6 [0x34f3a302d0]
  [1] _ZN20ComputeNonbondedUtil9calc_pairEP9nonbonded+0x239b  [0x596ee7]
  [2] _ZN20ComputeNonbondedPair7doForceEPP8CompAtomPP11CompAtomExtPP7Results+0xa35  [0x59185f]
  [3] _ZN16ComputePatchPair6doWorkEv+0xa7  [0x73ab63]
  [4] _ZN11WorkDistrib12enqueueWorkBEP12LocalWorkMsg+0x16  [0x9a43be]
  [5] _ZN19CkIndex_WorkDistrib31_call_enqueueWorkB_LocalWorkMsgEPvP11WorkDistrib+0xf  [0x9a43a5]
  [6] CkDeliverMessageFree+0x21  [0xa343cb]
  [7] _Z15_processHandlerPvP11CkCoreState+0x530  [0xa339bc]
  [8] CsdScheduleForever+0xa5  [0xabd4b9]
  [9] CsdScheduler+0x1c  [0xabd0ba]
  [10] _Z11master_initiPPc+0x2d6  [0x512386]
  [11] _ZN7BackEnd4initEiPPc+0x31  [0x5120a9]
  [12] main+0x2f  [0x50d99f]
  [13] __libc_start_main+0xf4  [0x34f3a1d994]
  [14] _ZNSt8ios_base4InitD1Ev+0x52  [0x508d5a]

and this in a second simulation
Stack Traceback:
  [0] /lib64/libc.so.6 [0x34f3a302d0]
  [1] _ZN20ComputeNonbondedUtil9calc_pairEP9nonbonded+0x21ac  [0x536f6c]
  [2] _ZN20ComputeNonbondedPair7doForceEPP8CompAtomPP7Results+0x5da  [0x52fc9e]
  [3] _ZN16ComputePatchPair6doWorkEv+0x85  [0x615dd1]
  [4] _ZN11WorkDistrib12enqueueWorkAEP12LocalWorkMsg+0x16  [0x728cd6]
  [5] _ZN19CkIndex_WorkDistrib31_call_enqueueWorkA_LocalWorkMsgEPvP11WorkDistrib+0xf  [0x728cbd]
  [6] CkDeliverMessageFree+0x21  [0x786a6b]
  [7] _Z15_processHandlerPvP11CkCoreState+0x455  [0x786075]
  [8] CsdScheduleForever+0xa2  [0x7f18a2]
  [9] CsdScheduler+0x1c  [0x7f14a0]
  [10] _Z10slave_initiPPc+0x10  [0x4baea4]
  [11] _ZN7BackEnd4initEiPPc+0x28f  [0x4bae89]
  [12] main+0x47  [0x4b67ef]
  [13] __libc_start_main+0xf4  [0x34f3a1d994]
  [14] _ZNSt8ios_base4InitD1Ev+0x3a  [0x4b2b5a]

in the start of the log file i get a warning i do not know if this warning is related to the abortion of my runs.
Charm warning> Randomization of stack pointer is turned on in Kernel, run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it. Thread migration may not work!
i have ran the line that it is refered  at the start of the log file (echo...) from the terminal as root, but i continue to get the same stack error and all my jobs continue to become aborted.
I would be grateful if you could provide me  some help!!

Stefanos pentas

Charm++> cpu topology info is being gathered.
Charm++> Running on 1 unique compute nodes (4-way SMP).
Info: NAMD 2.7b2 for Linux-x86_64
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60103 for net-linux-x86_64-iccstatic
Info: Built Thu Nov 12 22:12:21 CST 2009 by jim on belfast.ks.uiuc.edu
Info: 1 NAMD  2.7b2  Linux-x86_64  4    localhost.localdomain  root
Info: Running on 4 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.038754 s
Info: 1.63213 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is a2eq4.txt
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               2
Info: NUMBER OF STEPS        0
Info: STEPS PER CYCLE        10
Info: LOAD BALANCE STRATEGY  New Load Balancers -- ASB
Info: LDB PERIOD             2000 steps
Info: FIRST LDB TIMESTEP     50
Info: LAST LDB TIMESTEP     -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS    20
Info: MAX PAIR PARTITIONS    8
Info: SELF PARTITION ATOMS   154
Info: SELF2 PARTITION ATOMS   154
Info: PAIR PARTITION ATOMS   318
Info: PAIR2 PARTITION ATOMS  637
Info: MIN ATOMS PER PATCH    100
Info: INITIAL TEMPERATURE    600
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR       1
Info: DCD FILENAME           a2eq4.dcd
Info: DCD FREQUENCY          500
Info: DCD FIRST STEP         500
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME        a2eq4
Info: RESTART FILENAME       a2eq4.restart
Info: RESTART FREQUENCY      500
Info: SWITCHING ACTIVE
Info: SWITCHING ON           10
Info: SWITCHING OFF          12
Info: PAIRLIST DISTANCE      13.5
Info: PAIRLIST SHRINK RATE   0.01
Info: PAIRLIST GROW RATE     0.01
Info: PAIRLIST TRIGGER       0.3
Info: PAIRLISTS PER CYCLE    2
Info: PAIRLISTS ENABLED
Info: MARGIN                 0
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        16
Info: ENERGY OUTPUT STEPS    100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    1000
Info: PRESSURE OUTPUT STEPS  100
Info: SPHERICAL BOUNDARY CONDITIONS ACTIVE
Info: RADIUS #1              40
Info: FORCE CONSTANT #1      10
Info: EXPONENT #1            2
Info: SPHERE BOUNDARY CENTER(0, 0, 0)
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   600
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info:         ERROR TOLERANCE : 1e-08
Info:          MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED     1268422196
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         a2eq3.pdb
Info: STRUCTURE FILE         a2.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS             par_all27_prot_na_urea.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 250 BONDS
Info: 624 ANGLES
Info: 1050 DIHEDRAL
Info: 74 IMPROPER
Info: 0 CROSSTERM
Info: 130 VDW
Info: 0 VDW_PAIRS
Info: TIME FOR READING PSF FILE: 0.342469
Info: TIME FOR READING PDB FILE: 0.046067
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 25385 ATOMS
Info: 19186 BONDS
Info: 17606 ANGLES
Info: 13731 DIHEDRALS
Info: 2862 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 20807 RIGID BONDS
Info: 55348 DEGREES OF FREEDOM
Info: 9999 HYDROGEN GROUPS
Info: TOTAL MASS = 165378 amu
Info: TOTAL CHARGE = 3.76869e-05 e
Info: *****************************
Info:
Info: Entering startup at 0.470892 s, 8.29982 MB of memory in use
Info: Startup phase 0 took 0.034914 s, 8.29991 MB of memory in use
Info: Startup phase 1 took 0.091989 s, 12.4677 MB of memory in use
Info: Startup phase 2 took 0.036057 s, 12.6648 MB of memory in use
Info: PATCH GRID IS 4 BY 4 BY 4
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0.00509809 0.0202283 -0.00759836
Info: LARGEST PATCH (39) HAS 563 ATOMS
Info: CREATING 1250 COMPUTE OBJECTS
Info: Startup phase 3 took 0.116038 s, 15.8826 MB of memory in use
Info: Startup phase 4 took 0.0359981 s, 15.8825 MB of memory in use
Info: Startup phase 5 took 0.064003 s, 13.5387 MB of memory in use
LDB: Measuring processor speeds ... Done.
Info: Startup phase 6 took 1.20407 s, 13.5669 MB of memory in use
Info: CREATING 1250 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 1.69407e-21 AT 11.9974
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.13046e-16 AT 11.9974
Info: Startup phase 7 took 0.048105 s, 15.3198 MB of memory in use
Info: Startup phase 8 took 0.000268936 s, 17.0862 MB of memory in use
Info: Finished startup at 2.10233 s, 17.0862 MB of memory in use

REINITIALIZING VELOCITIES AT STEP 0 TO 600 KELVIN.
TCL: Running for 100000000 steps
PRESSURE: 0 0 0 0 0 0 0 0 0 0
GPRESSURE: 0 0 0 0 0 0 0 0 0 0
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP      POTENTIAL         TOTAL3        TEMPAVG

ENERGY:       0      4314.4789      7753.0739      3137.5824       867.4275        -166988.2096      2204.2726       107.7347         0.0000     33420.6082        -115183.0313       607.7190   -148603.6395   -114997.3554       607.7190

LDB: ============= START OF LOAD BALANCING ============== 6.78262
LDB: ============== END OF LOAD BALANCING =============== 6.78282

Info: Initial time: 4 CPUs 0.0902221 s/step 0.522119 days/ns 28.1713 MB memory
LDB: ============= START OF LOAD BALANCING ============== 11.4016
LDB: TIME 11.4027 LOAD: AVG 3.88616 MAX 4.60915  PROXIES: TOTAL 57 MAXPE 22 MAXPATCH 3 None 0.519055
LDB: TIME 11.4042 LOAD: AVG 3.88616 MAX 4.66338  PROXIES: TOTAL 90 MAXPE 34 MAXPATCH 3 TorusLB 0.519055
LDB: TIME 11.4241 LOAD: AVG 3.88616 MAX 4.07946  PROXIES: TOTAL 90 MAXPE 34 MAXPATCH 3 TorusLB 0.519055
LDB: ============== END OF LOAD BALANCING =============== 11.4329

PRESSURE: 100 0 0 0 0 0 0 0 0 0
GPRESSURE: 100 0 0 0 0 0 0 0 0 0
PRESSAVG: 100 0 0 0 0 0 0 0 0 0
GPRESSAVG: 100 0 0 0 0 0 0 0 0 0
Info: Initial time: 4 CPUs 0.089551 s/step 0.518235 days/ns 29.0045 MB memory
ENERGY:     100      4345.4452      8004.8547      3161.5787       928.3700        -167410.1654      2403.8067       106.7217         0.0000     33393.7236        -115065.6649       607.2301   -148459.3886   -114860.3031       601.4117

LDB: ============= START OF LOAD BALANCING ============== 16.0638
LDB: TIME 16.0649 LOAD: AVG 4.09756 MAX 4.37523  PROXIES: TOTAL 57 MAXPE 22 MAXPATCH 3 None 0.595697
LDB: TIME 16.0663 LOAD: AVG 4.09756 MAX 4.29352  PROXIES: TOTAL 90 MAXPE 34 MAXPATCH 3 RefineTorusLB 0.595697
LDB: ============== END OF LOAD BALANCING =============== 16.0682

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